Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.23 kDa 
• Atom Count: 6314 
• Modelled Residue Count: 620 
• Deposited Residue Count: 678 
• Unique protein chains: 1

4D5D

Crystal structure of CymA from Klebsiella oxytoca

• DOI: 10.2210/pdb4D5D/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Klebsiella oxytoca
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2014-11-03 Released: 2015-06-03 
• Deposition Author(s): van den Berg, B., Bhamidimarri, S.P., Kleinekathoefer, U., Winterhalter, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.198 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Literature

Outer-membrane translocation of bulky small molecules by passive diffusion.

van den Berg, B., Prathyusha Bhamidimarri, S., Dahyabhai Prajapati, J., Kleinekathofer, U., Winterhalter, M.

(2015) Proc Natl Acad Sci U S A 112: E2991-E2999

• PubMed: 26015567 
• DOI: 10.1073/pnas.1424835112
• Primary Citation of Related Structures:  
  4D51, 4D5B, 4D5D, 4V3G, 4V3H


• PubMed Abstract: 
  

The outer membrane (OM) of gram-negative bacteria forms a protective layer around the cell that serves as a permeability barrier to prevent unrestricted access of noxious substances. The permeability barrier of the OM results partly from the limited pore diameters of OM diffusion channels. As a consequence, there is an "OM size-exclusion limit," and the uptake of bulky molecules with molecular masses of more than ∼ 600 Da is thought to be mediated by TonB-dependent, active transporters. Intriguingly, the OM protein CymA from Klebsiella oxytoca does not depend on TonB but nevertheless mediates efficient OM passage of cyclodextrins with diameters of up to ∼ 15 Å. Here we show, by using X-ray crystallography, molecular dynamics simulations, and single-channel electrophysiology, that CymA forms a monomeric 14-stranded β-barrel with a large pore that is occluded on the periplasmic side by the N-terminal 15 residues of the protein. Representing a previously unidentified paradigm in OM transport, CymA mediates the passive diffusion of bulky molecules via an elegant transport mechanism in which a mobile element formed by the N terminus acts as a ligand-expelled gate to preserve the permeability barrier of the OM.

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Organizational Affiliation: 

School of Engineering and Science, Jacobs University Bremen, 28759 Bremen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYMA	A, B	339	Klebsiella oxytoca	Mutation(s): 0  Gene Names: cymA Membrane Entity: Yes
UniProt
Find proteins for Q48391 (Klebsiella oxytoca) Explore Q48391  Go to UniProtKB:  Q48391

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
Cyclohexakis-(1-4)-(alpha-D-glucopyranose)	C, E	6		N/A
Glycosylation Resources
GlyTouCan:  G22307HL GlyCosmos:  G22307HL

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)	D, F	7		N/A
Glycosylation Resources
GlyTouCan:  G01435GL GlyCosmos:  G01435GL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8E (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900015	C, E	alpha-cyclodextrin	Oligosaccharide / Drug delivery		Ligand Interaction

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900012	D, F	beta-cyclodextrin	Oligosaccharide / Drug delivery		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.198 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.16	α = 90
b = 77.991	β = 90
c = 109.927	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2014-11-03 
• Released Date: 2015-06-03 
Deposition Author(s): van den Berg, B., Bhamidimarri, S.P., Kleinekathoefer, U., Winterhalter, M.

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2015-06-10
  Changes: Source and taxonomy
• Version 1.2: 2015-06-24
  Changes: Database references
• Version 1.3: 2018-02-21
  Changes: Advisory, Database references, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary